Atom Nomenclature for TIG

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for TIG

Atom Name (V3) Atom Name (V2)
C C
N2 N
O O
C1 C1
N N1
C2 C2
CA CA
CB CB
CG CG
CD1 CD1
CD2 CD2
NE1 NE1
CE2 CE2
CE3 CE3
CH2 CH2
CZ2 CZ2
CZ3 CZ3
OXT OXT
H1 H1
H HN1
H2 HN1A
H2B H2
H2A H2A
HA HA
HB HB
HBA HBA
HD1 HD1
HE3 HE3
HH2 HH2
HZ2 HZ2
HZ3 HZ3
HNE1 HNE1
H15 H15
H16 H16
HXT HXT